Pärnänen Katariina, Karkman Antti, Tamminen Manu, Lyra Christina, Hultman Jenni, Paulin Lars, Virta Marko
University of Helsinki, Department of Food and Environmental Sciences, POB 56, 00014 University of Helsinki, Finland.
University of Helsinki, Department of Biosciences, POB 65, 00014 University of Helsinki, Finland.
Sci Rep. 2016 Oct 21;6:35790. doi: 10.1038/srep35790.
Antibiotic resistance genes are ubiquitous in the environment. However, only a fraction of them are mobile and able to spread to pathogenic bacteria. Until now, studying the mobility of antibiotic resistance genes in environmental resistomes has been challenging due to inadequate sensitivity and difficulties in contig assembly of metagenome based methods. We developed a new cost and labor efficient method based on Inverse PCR and long read sequencing for studying mobility potential of environmental resistance genes. We applied Inverse PCR on sediment samples and identified 79 different MGE clusters associated with the studied resistance genes, including novel mobile genetic elements, co-selected resistance genes and a new putative antibiotic resistance gene. The results show that the method can be used in antibiotic resistance early warning systems. In comparison to metagenomics, Inverse PCR was markedly more sensitive and provided more data on resistance gene mobility and co-selected resistances.
抗生素抗性基因在环境中普遍存在。然而，其中只有一小部分具有移动性并能够传播到病原菌中。到目前为止，由于基于宏基因组方法的灵敏度不足和重叠群组装困难，研究环境抗性组中抗生素抗性基因的移动性一直具有挑战性。我们开发了一种基于反向PCR和长读长测序的新方法，该方法成本低且省力，用于研究环境抗性基因的移动潜力。我们对沉积物样本应用了反向PCR，并鉴定出79个与所研究的抗性基因相关的不同移动遗传元件（MGE）簇，包括新型移动遗传元件、共选择抗性基因和一个新的假定抗生素抗性基因。结果表明，该方法可用于抗生素抗性预警系统。与宏基因组学相比，反向PCR的灵敏度明显更高，并提供了更多关于抗性基因移动性和共选择抗性的数据。
